Formalin-fixed archival tissues represent an invaluable resource for genetic and gene expression analysis, as they are the most widely available materials for studies of human disease. Tissue samples collected during medical procedures, such as surgery and biopsies, are often fixed in formalin, followed by embedding in paraffin for long-term preservation and archival storage. It is estimated that there were over 300 million of these formalin-fixed, paraffin-embedded (FFPE) samples archived in North America for cancer alone in 1999, with more samples accumulating at a rate of over 20 million per year. Many of these samples represent clinical outcomes with the potential to provide critical insight into expression profiles of biomarkers associated with the development of complex diseases. However, FFPE archival samples are considered poor material for PCR analytical applications due to chemical modification and cross-linking of, as well as substantial degradation of, nucleic acids. Targeting RNA extracted from FFPE specimens is a particular challenge since degradation can result in an average template size well below 200 nucleotides, and loss of poly-A tracts.